1V8Z

X-ray crystal structure of the Tryptophan Synthase b2 Subunit from Hyperthermophile, Pyrococcus furiosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors

Hioki, Y.Ogasahara, K.Lee, S.J.Ma, J.Ishida, M.Yamagata, Y.Matsuura, Y.Ota, M.Ikeguchi, M.Kuramitsu, S.Yutani, K.

(2004) Eur.J.Biochem. 271: 2624-2635

  • DOI: 10.1111/j.1432-1033.2004.04191.x

  • PubMed Abstract: 
  • The structure of the tryptophan synthase beta2 subunit (Pfbeta2) from the hyperthermophile, Pyrococcus furiosus, was determined by X-ray crystallographic analysis at 2.2 A resolution, and its stability was examined by DSC. This is the first report of ...

    The structure of the tryptophan synthase beta2 subunit (Pfbeta2) from the hyperthermophile, Pyrococcus furiosus, was determined by X-ray crystallographic analysis at 2.2 A resolution, and its stability was examined by DSC. This is the first report of the X-ray structure of the tryptophan synthase beta2 subunit alone, although the structure of the tryptophan synthase alpha2beta2 complex from Salmonella typhimurium has already been reported. The structure of Pfbeta2 was essentially similar to that of the beta2 subunit (Stbeta2) in the alpha2beta2 complex from S. typhimurium. The sequence alignment with secondary structures of Pfbeta and Stbeta in monomeric form showed that six residues in the N-terminal region and three residues in the C-terminal region were deleted in Pfbeta, and one residue at Pro366 of Stbeta and at Ile63 of Pfbeta was inserted. The denaturation temperature of Pfbeta2 was higher by 35 degrees C than the reported values from mesophiles at approximately pH 8. On the basis of structural information on both proteins, the analyses of the contributions of each stabilization factor indicate that: (a) the higher stability of Pfbeta2 is not caused by either a hydrophobic interaction or an increase in ion pairs; (b) the number of hydrogen bonds involved in the main chains of Pfbeta is greater by about 10% than that of Stbeta, indicating that the secondary structures of Pfbeta are more stabilized than those of Stbeta and (c) the sequence of Pfbeta seems to be better fitted to an ideally stable structure than that of Stbeta, as assessed from X-ray structure data.


    Organizational Affiliation

    Institute for Protein Research, Osaka University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophan synthase beta chain 1
A, B, C, D
388Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: trpB1
EC: 4.2.1.20
Find proteins for Q8U093 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U093
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C, D
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.835α = 90.00
b = 110.530β = 90.00
c = 159.999γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance